Although I can't give you a specific solution, I can tell you that it's possible. The company I work for does newspaper ads with many versions. They get a base color PDF, and a black-only PDF for each version (usually just price differences between similar stores). We use a program that essentially emulates a double-burn, where a new PDF is made that combines the CMY of the base with the K of the version, so I imagine that would also work in your situation. I don't work on that end of the jobs here, or I'd give you more detail.

I think I'd place both PDFs into a new ID file and in the Attibutes panel set the varnish to overprint fill. Hopefully it's tagged with a spot color so it will separate. Export a new PDF from the new doc.

Yes, it can be done in Acrobat. First show Layers Panel in Acrobat X > View > Show/Hide > Navigation Panes > Layers. Then in the Panel, select Options > Import as Layer > Source File [Varnish PDF] this will merge two pdfs into one page. Note: this can be done in earlier versions, the menu locations are slightly different.